It is no secret that our physical world is rapidly changing. Scientists have been working for decades to measure and define the huge changes that will characterize our environment in the years to come, and in doing so, have been able to provide us some clear images of the future—ice caps will be smaller, temperatures will be warmer, and sea levels will be higher.
However, while such forecasts give us a strong idea of how the environment is going to change, they don’t necessarily answer one important question: how are these changes to the environment going to affect the things living in it?
To understand how biological communities will change in the future, it is first necessary to accurately describe both their present and past conditions. In fact, the entire field of biology is rooted on this approach, with fundamental theories of evolution and biogeography originally formed from comparative studies of organisms, based largely on morphological observations of living organisms and ancient fossils.
Such interpretations of natural history were historically limited to organisms that can be observed and categorized visually, whether with the naked eye or under a microscope. However, in recent decades, basic biological concepts, such as what constitutes an individual organism, have been radically altered by an increasing appreciation for the complex interactions between larger organisms and their diverse microbial companions—mainly bacteria and archaea that, while invisible to the naked eye, play fundamental roles in altering biological resources within organisms and in their external environment1.
Thus, to fully understand how biodiversity patterns are shifting in an era of environmental change, biologists need to study organisms from every slice of life—from the largest predators down to the smallest microbe.
Researchers based at the Clemente Estable Institute of Biological Research in Uruguay are doing just that. Harnessing the power of Next-Generation metagenomic sequencing technology, Dr. Claudia Piccini and her collaborators recently published a paper in which they examined the effects of changes in glaciers on the ancient microbial communities of Antarctica2.
Antarctic lake sediments hold valuable information on biological communities of the past.
More specifically, Piccini and collaborators wanted to know exactly how local aquatic prokaryotes, that is, microscopic bacteria and archaea, reacted to glacial retreat over time. To ask this novel question, the researchers had to tackle the challenge of obtaining and analyzing information on what these prokaryotic communities looked like at different stages of glacial retreat.
Piccini and colleagues accomplished this by first taking sediment cores from an area in Antarctica believed to have previously held glacial ice before melting into a proglacial lake. Then, in order to obtain biological data from the time period represented in this sediment, they extracted the fragile, ancient DNA present in these sediment cores. Once the DNA was extracted, the next step was to proceed with 16S metabarcoding and library preparation, before proceeding to 16S amplicon sequencing at Novogene using NovaSeq platform (PE250).
By generating millions of reads of DNA sequences from the 16S region of the rRNA gene, which is commonly shared between prokaryotes, Piccini and collaborators could then use bioinformatic analysis to compare the differences between these reads with databases and identify what species were present in different sections of sediment, and therefore, at different periods in time. This methodology allows access to information that permits meaningful analysis of microbial communities consisting of thousands of species of prokaryotes––something which was inconceivable only a few decades ago.
By combining analysis of ancient sedimentary DNA with lithology, chronology, and geochemistry, the researchers were able to reconstruct what the microbial communities looked like in their study area over a period of thousands of years in which glaciers were progressively receding.
Through this reconstruction, it became clear how prokaryotic communities changed in response to glacial presence. In the earliest period of their analysis, prokaryotic communities were less diverse in their study area, and consisted of taxa that are associated with terrestrial environments2.
Over the course of thousands of years, as the glacial ice melted and formed a lake over the soil, a transitionary period of increasing prokaryotic diversity and changing nutrient conditions occurred from between approximately 4000 years to 2500 years ago2. Then, in the period from 2500 to 1000 years ago, the area appeared to be dominated by the highest diversity of prokaryotic taxa, and a community that was clearly associated with aquatic environments, indicating a complete transition from glacier-covered land to a freshwater lake environment2. Furthermore, the authors found that this increased microbial diversity was further marked by an increased trend towards generalist species. In other words, as the glacier retreated, the area became dominated by a more diverse array of species that were not necessarily specially adapted to glacial conditions.
The findings of this study are important because, despite the fact that we cannot see them, microbial communities play important roles in the functioning of all ecosystems3. In particular, aquatic prokaryotes play important roles in the movement of nutrients, such as carbon and nitrogen, through the environment2; these nutrients are important not only for the other, larger organisms that live in these habitats, but also for the cycling of nutrient systems between the Earth and its atmosphere4.
Understanding how these microbial systems respond to changes and fluctuations in environmental conditions improves our understanding of how the environment and the biological communities living in it will change over time—and, importantly, what these changes mean for our own future as humans.
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